Copilot custom agent always shows edit uncheckmarked in tools configuration window (WSL native install)

Type: Bug

## Environment Note

**NOTE:** This is a WSL Native install in Ubuntu 24.04 - NOT a remote session into WSL from Windows. It uses WSLg to create a native windows display for VS Code. It is very close to a native Ubuntu install.

See bottom for full environment details

## Issue summary

The agent tool configuration box that pops up when you click the configure icon to the right of the model selector ALWAYS shows all the "edit" group boxes empty when it opens. If you select any of them and select "OK", it will add them correctly into the agent `tools` frontmatter

## Examples:

Example - adding several subboxes under "edit" and hitting OK yields:

```yaml
tools: [execute, read, edit/createDirectory, edit/createFile, edit/editFiles, edit/rename, search, vscodeGeneral/rename]
```

if you just select the top-level edit box, hitting "OK" will set just `edit`:

```yaml
tools: [execute, read, edit, search]
```

But every time you reopen the box, all the edit items are empty. And if you hit "OK" with them still empty, it will remove them from the `tools` frontmatter.

```yaml
tools: [execute, read, search]
```

## Possible related `apply_patch` command issue

I'm not sure if this is related, but in WSL with a native WSL/linux install (Ubuntu 24.04 via apt), in the configuration described above (using a custom agent file in ~/.copilot/agents), it has started complaining that the "apply_patch" command is not found. It's trying to run this directly in the terminal:

```sh
Command 'apply_patch' not found, did you mean:
```

which forces it to do workarounds and waste tokens/take longer as a result.

I don't know if the two are related - i.e. if the edit is actually failing to apply in the tools, is that why apply_patch is not available?

## Base Environment

VS Code version: Code 1.129.0 (125df4672b8a6a34975303c6b0baa124e560a4f7, 2026-07-15T00:08:44Z)
OS version: Linux x64 6.18.33.2-microsoft-standard-WSL2
Modes:

System Info

|Item|Value|
|---|---|
|CPUs|13th Gen Intel(R) Core(TM) i7-13850HX (28 x 0)|
|GPU Status|2d_canvas: unavailable_software
GPU0: VENDOR= 0x0000 [Google Inc. (Mesa)], DEVICE=0x0000 [ANGLE (Mesa, llvmpipe (LLVM 20.1.2 256 bits), OpenGL ES 3.2 Mesa 25.2.8-0ubuntu0.24.04.2)], DRIVER_VENDOR=Mesa, DRIVER_VERSION=25.2.8 *ACTIVE*
Machine model name:
Machine model version:
direct_rendering_display_compositor: disabled_off_ok
gpu_compositing: disabled_software
multiple_raster_threads: enabled_on
opengl: unavailable_off
rasterization: unavailable_off
raw_draw: disabled_off_ok
skia_graphite: disabled_off
trees_in_viz: disabled_off
video_decode: unavailable_off
video_encode: disabled_software
vulkan: disabled_off
webgl: unavailable_off
webgpu: unavailable_software
webgpu_on_vk_via_gl_interop: disabled_off
webnn: disabled_off|
|Load (avg)|1, 0, 0|
|Memory (System)|31.17GB (12.06GB free)|
|Process Argv|--crash-reporter-id 630421af-3033-4c62-b1a6-2e9700913eb0|
|Screen Reader|no|
|VM|0%|
|DESKTOP_SESSION|undefined|
|XDG_CURRENT_DESKTOP|GNOME|
|XDG_SESSION_DESKTOP|undefined|
|XDG_SESSION_TYPE|wayland|
Extensions (33)

Name|Identifier|Author|Version
---|---|---|---
Better Comments|aaron-bond.better-comments|aaron-bond|3.0.2
ty|astral-sh.ty|astral-sh|2026.62.0
Mermaid Markdown Syntax Highlighting|bpruitt-goddard.mermaid-markdown-syntax-highlighting|bpruitt-goddard|1.8.1
Ruff|charliermarsh.ruff|charliermarsh|2026.62.0
Draw.io Integration: Markdown plugin|dzylikecode.vscode-drawio-plugin-markdown|dzylikecode|0.3.5
Git Opener|foshati.git-opener|Foshati|1.1.5
Draw.io Integration|hediet.vscode-drawio|hediet|1.9.0
PlantUML|jebbs.plantuml|jebbs|2.18.1
AHK++ (AutoHotkey Plus Plus)|mark-wiemer.vscode-autohotkey-plus-plus|mark-wiemer|6.7.3
MATLAB|mathworks.language-matlab|MathWorks|1.3.12
Rainbow CSV|mechatroner.rainbow-csv|mechatroner|3.24.1
Git Graph|mhutchie.git-graph|mhutchie|1.30.0
XML Format|mikeburgh.xml-format|mikeburgh|1.1.3
Container Tools|ms-azuretools.vscode-containers|ms-azuretools|2.4.5
.NET Install Tool|ms-dotnettools.vscode-dotnet-runtime|ms-dotnettools|3.1.0
Python Debugger|ms-python.debugpy|ms-python|2026.6.0
Python|ms-python.python|ms-python|2026.4.0
Pylance|ms-python.vscode-pylance|ms-python|2026.2.1
Python Environments|ms-python.vscode-python-envs|ms-python|1.36.0
Dev Containers|ms-vscode-remote.remote-containers|ms-vscode-remote|0.466.0
Remote - SSH|ms-vscode-remote.remote-ssh|ms-vscode-remote|0.124.0
Remote - SSH: Editing Configuration Files|ms-vscode-remote.remote-ssh-edit|ms-vscode-remote|0.87.0
WSL|ms-vscode-remote.remote-wsl|ms-vscode-remote|0.104.3
Remote Development|ms-vscode-remote.vscode-remote-extensionpack|ms-vscode-remote|0.26.0
Remote Explorer|ms-vscode.remote-explorer|ms-vscode|0.5.0
Remote - Tunnels|ms-vscode.remote-server|ms-vscode|1.5.3
Paste Image|mushan.vscode-paste-image|mushan|1.0.4
Draw.io Integration: Mermaid plugin|nopeslide.vscode-drawio-plugin-mermaid|nopeslide|0.1.5
XML|redhat.vscode-xml|redhat|0.29.3
CSV|repreng.csv|ReprEng|1.3.0
Xml Complete|rogalmic.vscode-xml-complete|rogalmic|0.3.0
Even Better TOML|tamasfe.even-better-toml|tamasfe|0.21.2
Mermaid Editor|tomoyukim.vscode-mermaid-editor|tomoyukim|0.19.1

A/B Experiments

```
vsliv368cf:30146710
binariesv615:30325510
nativeloc1:31344060
dwcopilot:31170013
dwoutputs:31242946
copilot_t_ci:31333650
e5gg6876:31282496
pythonrdcb7:31342333
6518g693:31463988
aj953862:31281341
6abeh943:31336334
envsactivate1:31551504
cloudbuttont:31379625
42190218_ostrepl:31403339
ddidt:31399633
ec5jj548:31422691
cp_cls_t_966_ss:31526232
4je02754:31466945
8hhj4413:31478653
ge8j1254_inline_auto_hint_haiku:31490510
38bie571_auto:31478677
cp_cls_c_1081:31454833
conptydll_true:31498968
e9c30283:31461165
test_control1:31471004
c9b86496:31447327
capico_a_098a3278:31551523
idci7584:31464702
e3e4d672:31494082
ei9d7968:31496641
nes-extended-on:31455476
chat:31457767
8hig5102:31480529
89g7j272:31518289
7e187181:31503455
i2gc6536:31499202
52612955:31516516
ghj88844:31499326
ddid_t:31478206
hmra_i5g22:31518061
ie3bb177:31543534
7df3h592:31512476
cp_cls_t_1082:31535311
logging_enabled_new:31498466
db5d2638:31499441
jb_cp_cls_t_632:31543129
56dj4588:31512888
32d76977:31512328
ha629193:31508444
cdk-lw-on:31524445
f9bf7985:31543584
a1ije391_t:31540920
g4a0e106:31529594
41836166:31537719
prpt_lrg:31518466
jbcp_cls_pctr_t:31531130
61138546:31518536
cp_intellij_t_nes:31548657
d7b18187:31526828
nes-curr-leftover-1500:31538366
h561g132:31533256
session_8:31532895
ihg5j128:31534457
f412h606:31551416
9gg7f176:31542112
sandbox-ui-on-2:31543161
7642ad28:31552287
6i51c363:31551401

```